How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques,ACS Catalysis

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How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques
ACS Catalysis ( IF 11.3 ) Pub Date : 2023-06-01 , DOI: 10.1021/acscatal.3c01473
Sudip Das ₁ , Umberto Raucci ₁ , Rui P. P. Neves ₂ , Maria J. Ramos ₂ , Michele Parrinello ₁

Affiliation

Enzymatic catalysis is a complex process that can involve multiple conformations of the enzyme:substrate complex and several competitive reaction pathways, resulting in a multi-dimensional free energy landscape. The study of enzymatic activity often requires deep knowledge of the system to establish the catalytic mechanism and identify the possible reactive conformations of the complex. Here, we present an enhanced sampling and machine learning-based approach to explore the catalytic reaction space and characterize the transformation from reactive to non-reactive conformations with minimal a priori knowledge of the system. We applied this approach to study the rate-determining step of the glycolysis reaction of maltopentose catalyzed by human pancreatic α-amylase, an important enzyme in glucose production as well as a major drug target for the treatment of type-II diabetes. We unravel the complexity of the enzymatic reaction, reveal three binding modes of the substrate within the active site, and highlight the role of water in the catalytic process and in the stepwise conversion of reaction-ready to non-reactive conformations. Overall, these insights offer atomistic details on the catalytic mechanism and dynamics of the active site, allowing one to shed light on two fundamental questions in enzymatic catalysis, that is how and when does an enzyme react?

中文翻译：

酶如何以及何时发生反应？通过增强的采样技术揭示 α-淀粉酶的催化活性

酶促催化是一个复杂的过程，可能涉及酶的多种构象：底物复合物和几种竞争性反应途径，从而产生多维自由能景观。酶活性的研究通常需要对系统有深入的了解，以建立催化机制并确定复合物可能的反应构象。在这里，我们提出了一种增强的采样和基于机器学习的方法来探索催化反应空间，并以最小的先验来表征从反应性构象到非反应性构象的转变系统知识。我们应用这种方法研究了人胰α-淀粉酶催化的麦芽糖戊糖糖酵解反应的限速步骤，人胰α-淀粉酶是葡萄糖生产中的重要酶，也是治疗 II 型糖尿病的主要药物靶点。我们揭示了酶促反应的复杂性，揭示了底物在活性位点内的三种结合模式，并强调了水在催化过程中的作用以及在准备好反应的构象逐步转化为非反应性构象中的作用。总的来说，这些见解提供了关于催化机制和活性位点动力学的原子细节，使人们能够阐明酶催化中的两个基本问题，即酶如何以及何时反应？

更新日期：2023-06-01

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